# SEnsible Step-wise Analysis of DNA MEthylation BeadChips

## Documentation for package ‘sesame’ version 1.12.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I M N O P Q R S T V misc

sesame-package | Analyze DNA methylation data

## -- A --

addMask | Add probes to mask
as.data.frame.sesameQC | Coerce a sesameQC into a dataframe
attachManifest | Annotate a data.frame using manifest

## -- B --

BetaValueToMValue | Convert beta-value to M-value
binSignals | Bin signals from probe signals
bisConversionControl | Compute internal bisulfite conversion control
bSubComplete | subset beta value matrix by complete probes
bSubMostVariable | Get most variable probes
bSubProbes | subset beta value matrix by probes

## -- C --

calcDatabaseSetStatistics1 | calcDatabaseSetStatistics1 calculates features of x
calcDatabaseSetStatisticsAll | calcDatabaseSetStatisticsAll builds dataset for a given betas matrix composed of engineered features from the given database sets
checkLevels | filter data matrix by factor completeness only works for discrete factors
chipAddressToSignal | Lookup address in one sample
cnSegmentation | Perform copy number segmentation
compareDatbaseSetOverlap | compareDatbaseSetOverlap calculates the pariwise overlap between given list of database sets using a distance metric.
compareMouseStrainReference | Compare Strain SNPs with a reference panel
compareMouseTissueReference | Compare mouse array data with mouse tissue references
controls | get the controls attributes
createDatabaseSetNetwork | createGeneNetwork creates databaseSet network using the Jaccard index.
createUCSCtrack | Turn beta values into a UCSC browser track

## -- D --

deIdentify | De-identify IDATs by removing SNP probes
detectionPnegEcdf | Detection P-value based on ECDF of negative control
detectionPoobEcdf | Detection P-value based on ECDF of out-of-band signal
detectionPoobEcdf2 | Detection P-value based on ECDF of out-of-band signal
diffRefSet | Restrict refset to differentially methylated probes use with care, might introduce bias
dmContrasts | List all contrasts of a DMLSummary
DML | Test differential methylation on each locus
DMR | Find Differentially Methylated Region (DMR)
dyeBiasCorr | Correct dye bias in by linear scaling.
dyeBiasCorrMostBalanced | Correct dye bias using most balanced sample as the reference
dyeBiasCorrTypeINorm | Dye bias correction by matching green and red to mid point
dyeBiasDistortion | Quantify how much dye bias in high signal range deviates from the global median
dyeBiasNL | Dye bias correction by matching green and red to mid point

## -- E --

estimateCellComposition | Estimate cell composition using reference
estimateLeukocyte | Estimate leukocyte fraction using a two-component model
extractDesign | Extract the first design category

## -- F --

formatVCF | Convert SNP from Infinium array to VCF file

## -- G --

getAFTypeIbySumAlleles | Get allele frequency treating type I by summing alleles
getAutosomeProbes | Get autosome probes
getBetas | Get beta Values
getBinCoordinates | Get bin coordinates
getDatabaseSetOverlap | getDatabaseSetOverlap tests for the overlap of set of probes (querySet) in a single given feature (database set)
getNormCtls | get normalization control signal
getProbesByChromosome | Get Probes by Chromosome
getProbesByGene | Get Probes by Gene
getProbesByRegion | Get probes by genomic region
getProbesByTSS | Get Probes by Gene Transcription Start Site (TSS)
getRefSet | Retrieve reference set
getSexInfo | Get sex-related information

## -- I --

inferEthnicity | Infer Ethnicity
inferInfiniumIChannel | Infer and reset color channel for Type-I probes instead of using what is specified in manifest. The results are stored to sdf@extra$IGG and sdf@extra$IRR slot.
inferSex | Infer Sex
inferSexKaryotypes | Infer Sex Karyotype
inferSpecies | Infer Species
inferStrain | Infer strain information for mouse array
inferTissue | inferTissue1 infers the tissue of a single sample (as identified through the branchIDs in the row data of the reference) by reporting independent composition through cell type deconvolution.
initFileSet | initialize a fileSet class by allocating appropriate storage
isUniqProbeID | Whether the probe ID is the uniq probe ID like in the mouse array, e.g., cg36609548

## -- M --

mapFileSet | Deposit data of one sample to a fileSet (and hence to file)
meanIntensity | Whole-dataset-wide Mean Intensity
medianTotalIntensity | Whole-dataset-wide Median Total Intensity (M+U)
MValueToBetaValue | Convert M-value to beta-value

## -- N --

neob | Negative control plus out-of-band background correction
noMasked | remove masked probes from SigDF
noob | Noob background correction

## -- O --

openSesame | The openSesame pipeline
openSesameToFile | openSesame pipeline with file-backed storage

## -- P --

plotLollipop | plotLollipop creates a lollipop plot of log(estimate) given data with fields estimate.
plotVolcano | plotVolcano creates a volcano plot of -log2(p.value) and log(estimate) given data with fields estimate and p.value.
pOOBAH | Detection P-value based on ECDF of out-of-band signal
pOOBAH2 | Detection P-value based on ECDF of out-of-band signal
predictAgeHorvath353 | Horvath 353 age predictor
predictAgeSkinBlood | Horvath Skin and Blood age predictor
predictMouseAgeInMonth | Mouse age predictor
print.DMLSummary | Print DMLSummary object
print.fileSet | Print a fileSet
print.sesameQC | Print sesameQC object
print.SigDF | Print SigDF object
probeID_designType | Extract the probe type field from probe ID This only works with the new probe ID system. See https://github.com/zhou-lab/InfiniumAnnotation for illustration
probeSuccessRate | Whole-dataset-wide Probe Success Rate

## -- Q --

qualityMask | Mask beta values by design quality
qualityRank | This function looks at public data of similar nature e.g., tissue, FFPE vs non-FFPE, etc to evaluate the quality of the target data quality

## -- R --

readFileSet | Read an existing fileSet from storage
readIDATpair | Import a pair of IDATs from one sample
reIdentify | Re-identify IDATs by restoring scrambled SNP intensities
reopenSesame | re-compute beta value for GenomicRatioSet
resetMask | Reset Masking
RGChannelSetToSigDFs | Convert RGChannelSet (minfi) to a list of SigDF (SeSAMe)

## -- S --

scrub | SCRUB background correction
scrubSoft | SCRUB background correction
sdfPlatform | Convenience function to output platform attribute of SigDF
sdf_read_table | read a table file to SigDF
sdf_write_table | write SigDF to table file
searchIDATprefixes | Identify IDATs from a directory
segmentBins | Segment bins using DNAcopy
sesame | Analyze DNA methylation data
sesamePlotIntensVsBetas | Plot Total Signal Intensities vs Beta Values This plot is helpful in revealing the extent of signal background and dye bias.
sesamePlotRedGrnQQ | Plot red-green QQ-Plot using Infinium-I Probes
sesameQC | Generate summary numbers that indicative of experiment quality Please provide a raw SigDF(before any preprocessing). Usually directly from readIDATpair
sesamize | "fix" an RGChannelSet (for which IDATs may be unavailable) with Sesame The input is an RGSet and the output is a sesamized minfi::GenomicRatioSet
setMask | Set mask to only the probes specified
setMaskBySpecies | Set mask using species-specific manifest
SigDF | SigDF constructor from a plain data frame
SigDFsToRGChannelSet | Convert sesame::SigDF to minfi::RGChannelSet
SigDFToRatioSet | Convert one sesame::SigDF to minfi::RatioSet
signalMU | report M and U for regular probes
sliceFileSet | Slice a fileSet with samples and probes
SNPcheck | Check sample identity using SNP probes
summaryExtractTest | Extract slope information from DMLSummary

## -- T --

testEnrichment | testEnrichment tests for the enrichment of set of probes (query set) in a number of features (database sets).
testEnrichment1 | testEnrichment1 tests for the enrichment of set of probes (query set) in a single given feature (database set)
testEnrichmentFGSEA | testEnrichmentFGSEA uses the FGSEA test to estimate the association of a categorical variable against a continuous variable.
testEnrichmentFisher | testEnrichmentFisher uses Fisher's exact test to estimate the association between two categorical variables.
testEnrichmentGene | testEnrichmentGene tests for the enrichment of set of probes (querySet) in gene regions.
testEnrichmentSpearman | testEnrichmentSpearman uses the Spearman statistical test to estimate the association between two continuous variables.
totalIntensities | M+U Intensities Array
twoCompsEst2 | Estimate the fraction of the 2nd component in a 2-component mixture

## -- V --

visualizeGene | Visualize Gene
visualizeProbes | Visualize Region that Contains the Specified Probes
visualizeRegion | Visualize Region
visualizeSegments | Visualize segments

## -- misc --

_PACKAGE | Analyze DNA methylation data